TestMAPlot

library(Glimma)
library(limma)
library(GlimmaV2)

data(lymphomaRNAseq)
rnaseq <- lymphomaRNAseq

# 7 samples
# each instance is a gene
# attribute is number of counts per sample
# data.frame(rnaseq$counts)

# add lane
groups <- data.frame(genotype=rnaseq$samples$group,
                     lane= as.character(c(rep(4,5),3,3)),
                     miscCont=c(rep(4000,5),300,250),
                     miscDisc=c("blue","red",rep("green",5)))

# add libsize
groups <- rnaseq$samples$group

# fit
design <- model.matrix(~0+groups)
contrasts <- cbind(Smchd1null.vs.WT=c(-1,1))

# convert raw counts to logCPM values by automatically extracting libsizes and normalisation factors from x
vm <- voomWithQualityWeights(rnaseq, design=design)
fit <- lmFit(vm, design=design)
fit <- contrasts.fit(fit, contrasts)
fit <- eBayes(fit)
dt <- decideTests(fit)
summary(dt)

##        Smchd1null.vs.WT
## Down               1478
## NotSig            24424
## Up                 1277

# log cpm is the attribute here
# averaged across all arrays in the original linear model fit
# each instance is a gene;
# the col vector names are the geneIDs
# the col vector attribute is mean expression
# data.frame(fit$Amean)


# for now assume fit object

# this is where info for the MD scatter plot comes from!
# data.frame(vm$E)
# fit$design

prepareXYData <- function(
  x,
  xvals=NULL,
  yvals=NULL,
  xlab=NULL,
  ylab=NULL,
  status=NULL)
{
  # assume MA plot if no x/y are given
  if (is.null(xvals) && is.null(yvals))
  {
    # for now assume fit object
    xvals <- unname(x$Amean)
    xlab <- "logcpm"
    yvals <- unname(x$coefficients[,1])
    ylab <- "logfc"
    stopifnot(all(names(x$Amean) == names(x$coefficients[,1])))
    table <- data.frame(xvals, yvals)
    names(table) <- c(xlab, ylab)
    table <- cbind(table, x$genes)
  }
  else
  {
    
  }
  data <- list(x=xlab, y=ylab, table=table, cols=colnames(table))
  return(list(plotType="XY", data=data))
}

rep(1,5)

## [1] 1 1 1 1 1

GlimmaV2("MA", fit, colour=dt, display.columns=c("PValue"))

## Warning in readLines(con): incomplete final line found on 'C:/Users/hkari/
## OneDrive/onenote/R/win-library/3.6/GlimmaV2/htmlwidgets/GlimmaV2.yaml'